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Detailed information for vg0420654451:

Variant ID: vg0420654451 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20654451
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTTGTTCCTGCTCGTGTTGCATCTTTGATCACATAATAACAGGCAATATTGTTTAAAATGATGTTGCTGCAAACCAAGAATAACTGGTTCAAAACAGT[G/A]
AGATTTTTCACTTGATTCTGAAGTAAATAAGCTTATTATTCTCTAACCTTTTTGTCAAAGAATACGTTGACGGGAAAAAAAACCACTGTTTGTCCTTTAT

Reverse complement sequence

ATAAAGGACAAACAGTGGTTTTTTTTCCCGTCAACGTATTCTTTGACAAAAAGGTTAGAGAATAATAAGCTTATTTACTTCAGAATCAAGTGAAAAATCT[C/T]
ACTGTTTTGAACCAGTTATTCTTGGTTTGCAGCAACATCATTTTAAACAATATTGCCTGTTATTATGTGATCAAAGATGCAACACGAGCAGGAACAACAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.60% 7.20% 0.19% 0.00% NA
All Indica  2759 98.70% 1.20% 0.11% 0.00% NA
All Japonica  1512 85.50% 14.20% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.50% 2.40% 0.17% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 98.00% 1.90% 0.13% 0.00% NA
Temperate Japonica  767 97.10% 2.70% 0.13% 0.00% NA
Tropical Japonica  504 74.20% 25.80% 0.00% 0.00% NA
Japonica Intermediate  241 72.20% 26.10% 1.66% 0.00% NA
VI/Aromatic  96 13.50% 85.40% 1.04% 0.00% NA
Intermediate  90 87.80% 12.20% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0420654451 G -> A LOC_Os04g34090.1 downstream_gene_variant ; 1656.0bp to feature; MODIFIER silent_mutation Average:71.969; most accessible tissue: Callus, score: 84.97 N N N N
vg0420654451 G -> A LOC_Os04g34100.1 intron_variant ; MODIFIER silent_mutation Average:71.969; most accessible tissue: Callus, score: 84.97 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420654451 NA 5.30E-07 mr1206 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420654451 NA 4.33E-07 mr1229 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420654451 NA 2.27E-07 mr1229 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420654451 3.07E-06 NA mr1238 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420654451 NA 9.48E-07 mr1596 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420654451 4.44E-06 4.43E-06 mr1753 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251